[BioC] snapCGH fails in runBioHMM

Tue May 12 17:55:35 CEST 2009

Dear John,

Thanks a lot!

Best,

R.

On Tuesday 12 May 2009 17:53:40 J-C. Marioni wrote:
> Dear Ramon,
>
> Sorry about the delay in responding to your messages - I was away last
> week. I suspect that some of the problems are due to the Namespace - I'll
> work on this today and upload a new version of the package later.
>
> Apologies for any inconvenince.
>
> John
>
> On Tue, 12 May 2009, Ramon Diaz-Uriarte wrote:
> > Dear Wolfgang,
> >
> > On Tuesday 12 May 2009 16:52:30 Wolfgang Raffelsberger wrote:
> >> Hi Ramon,
> >>
> >> just to say that I posted another message concerning an error with
> >> snapCGH package on this list on may 4th, but got no reply.
> >
> > Yes, I am expecting something similar. For my own particualr problem
> > (with package ADaCGH) I've just surrounded all calls to snapCGH functions
> > with a "try", so the help examples at least can run, and I return to the
> > user the error message that results from snapCGH.
> >
> >> I my case it was one particular array that for some reason caused
> >> runBioHMM() to stall.  I found a workaround, by just inverting R & G
> >> channel for the array causing the trouble and runBioHMM() ran fine (of
> >> course after segmentation I had to re-flip R&G for the array in
> >> question). Besides, I had and "fixed" another problem with runGLAD()
> >> that wasn't expecting snapCGH objects ...
> >>
> >> But I haven't tried the snapCGH v.1.12  yet ...
> >
> > As far as I can tell, there are no differences whatsoever in the code
> > itself between versions 1.11 and 1.12 (or between 1.12 and 1.13). 1.12
> > and 1.13 seem identical except for their version number.  1.12 and 1.11
> > differ in a few changes in the documentation (formatting changes and
> > fixes of types) and in the addition of the (buggy) NAMESPACE in 1.12.
> >
> > Best,
> >
> >
> > R.
> >
> >> cheers,
> >> Wolfgang
> >>
> >> Ramon Diaz-Uriarte a écrit :
> >>> Dear All,
> >>>
> >>> snapCGH (v. 1.12 in BioC 2.4 for sure; most likely v. 1.13 in BioC 2.5
> >>> too) fails with the error
> >>>
> >>> C symbol name "runNelderMead" not in DLL for package "snapCGH"
> >>>
> >>> The problem is that the NAMESPACE file is not loading the required
> >>> code. Sure enough, if one loads the .so file manually (e.g.,
> >>> via "dyn.load('path-to-library/snapCGH.so')") things work.
> >>>
> >>>
> >>> So, while the package gets fixed, what would be the orthodox way to get
> >>> packages that depend on snapCGH to work?
> >>>
> >>>
> >>> Best,
> >>>
> >>> R
> >>>
> >>> ************************
> >>>
> >>> Two reproducible examples:
> >>>
> >>> a) Using function fit.model (which is docummented but not exported in
> >>> the NAMESPACE, which is available since v. 1.12):
> >>>
> >>> ydat <- matrix(rnorm(100), ncol = 1)
> >>> datainfo <- data.frame(Name = 1:100, Chrom = rep(1, 100), Position =
> >>> 1:100)
> >>>
> >>> snapCGH:::fit.model(sample = 1, chrom = 1, dat = ydat,
> >>>                     datainfo = datainfo)
> >>>
> >>>
> >>>
> >>> b) Using the code in the vignette (the vignette does not fail, as the
> >>> crucial chunck has "eval=FALSE", and the help for runBioHMM has no
> >>> runnable examples):
> >>>
> >>> datadir <- system.file("testdata", package="snapCGH")
> >>> targets <- readTargets("targets.txt", path=datadir)
> >>> RG1 <- read.maimages(targets$FileName, path=datadir, source =
> >>> "genepix") RG1 <- read.clonesinfo("cloneinfo.txt", RG1, path=datadir)
> >>> RG1$printer <- getLayout(RG1$genes)
> >>> types <- readSpotTypes("SpotTypes.txt", path=datadir)
> >>> RG1$genes$Status <- controlStatus(types, RG1)
> >>> RG1$design <- c(-1,-1)
> >>> RG2 <- backgroundCorrect(RG1, method="minimum")
> >>> MA <- normalizeWithinArrays(RG2, method="median")
> >>> MA2 <- processCGH(MA,method.of.averaging=mean, ID = "ID")
> >>> SegInfo.Bio <- runBioHMM(MA2)
> >>>
> >>>> version
> >>>
> >>>                _
> >>> platform       x86_64-unknown-linux-gnu
> >>> arch           x86_64
> >>> os             linux-gnu
> >>> system         x86_64, linux-gnu
> >>> status         Patched
> >>> major          2
> >>> minor          9.0
> >>> year           2009
> >>> month          05
> >>> day            11
> >>> svn rev        48528
> >>> language       R
> >>> version.string R version 2.9.0 Patched (2009-05-11 r48528)
> >>>
> >>>> packageDescription("snapCGH")
> >>>
> >>> Package: snapCGH
> >>> Title: Segmentation, normalisation and processing of aCGH data.
> >>> Version: 1.12.0
> >>> Date: 2000-04-07
> >>> Author: Mike L. Smith, John C. Marioni, Steven McKinney, Thomas
> >>>         Hardcastle, Natalie P. Thorne
> >>> Description: Methods for segmenting, normalising and processing aCGH
> >>>         data; including plotting functions for visualising raw and
> >>>         segmented data for individual and multiple arrays.
> >>> biocViews: Microarray, DNACopyNumber, TwoChannel, Preprocessing
> >>> Maintainer: John Marioni <marioni at uchicago.edu>
> >>> Depends: limma,tilingArray,DNAcopy,GLAD,cluster,methods,aCGH
> >>> License: GPL
> >>> Packaged: 2009-04-21 09:40:04 UTC; biocbuild
> >>> Built: R 2.9.0; x86_64-unknown-linux-gnu; 2009-05-12 10:31:17 UTC; unix
> >>
> >> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
> >> Wolfgang Raffelsberger, PhD
> >> Laboratoire de BioInformatique et Génomique Intégratives
> >> CNRS UMR7104, IGBMC,
> >> 1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
> >> Tel (+33) 388 65 3300         Fax (+33) 388 65 3276
> >> wolfgang.raffelsberger (at) igbmc.fr
> >
> > --
> > Ramón Díaz-Uriarte
> > Biocomputing Programm
> > Centro Nacional de Investigaciones Oncológicas (CNIO)
> > (Spanish National Cancer Center)
> > Melchor Fernández Almagro, 3
> > 28029 Madrid (Spain)
> > Fax: +-34-91-224-6972
> > Phone: +-34-91-224-6900
> >
> > http://ligarto.org/rdiaz
> >
> >
> >
> >
> > **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y ...{{dropped:3}}
> >
> > _______________________________________________
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-- 
Ramón Díaz-Uriarte
Biocomputing Programm
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y ...{{dropped:3}}